python脚本和库，用于读取freesurfer&ashs计算的海马子域体积
freesurfer-volume-reader的Python项目详细描述
python脚本库，用于读取由 自由冲浪者
- 自由冲浪者 https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
- 灰烬https://sites.google.com/site/hipposubfields/home
安装
pip3 install --user freesurfer-volume-reader freesurfer-volume-reader --help
发布遵循semantic versioning 计划。
用法
自由曲面
exportSUBJECTS_DIR=/my/freesurfer/subjects freesurfer-volume-reader
或
freesurfer-volume-reader /my/freesurfer/subjects freesurfer-volume-reader /my/freesurfer/subjects /other/freesurfer/subjects
或
fromfreesurfer_volume_readerimportfreesurferforvolume_fileinfreesurfer.HippocampalSubfieldsVolumeFile.find('/my/freesurfer/subjects'):print(volume_file.subject,volume_file.hemisphere,volume_file.analysis_id)print(volume_file.read_volumes_mm3())print(volume_file.read_volumes_dataframe())
灰烬
exportSUBJECTS_DIR=/my/ashs/subjects freesurfer-volume-reader --source-types ashs
或
freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects /other/ashs/subjects
或
fromfreesurfer_volume_readerimportashsforvolume_fileinashs.HippocampalSubfieldsVolumeFile.find('/my/ashs/subjects'):print(volume_file.subject,volume_file.hemisphere,volume_file.correction)print(volume_file.read_volumes_mm3())print(volume_file.read_volumes_dataframe())
颅内容积
fromfreesurfer_volume_readerimportashsforvolume_fileinashs.IntracranialVolumeFile.find('/my/ashs/subjects'):print(volume_file.subject)print(volume_file.read_volume_mm3())print(volume_file.read_volume_series())
自由冲浪者
freesurfer-volume-reader --source-types ashs freesurfer-hipposf -- /my/subjects
freesurfer-volume-reader --source-types ashs freesurfer-hipposf -- /my/ashs/subjects /my/freesurfer/subjects /other/subjects
测试
pip3 install --user pipenv
git clone https://github.com/fphammerle/freesurfer-volume-reader.git
cd freesurfer-volume-reader
pipenv run pylint freesurfer_volume_reader
pipenv run pytest
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